Searching journal content for articles similar to Stewart et al. 14 (6): 1176.

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  1. Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
    • Wiesław Babik,
    • Katarzyna Dudek,
    • Gemma Palomar,
    • Marzena Marszałek,
    • Grzegorz Dubin,
    • Maximina H. Yun,
    • and Magdalena Migalska
    Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
    ...region indicated with dashed rectangles in the upper plot. MHC-I, MHC-II and APG are marked and labeled individually, with the width of rectangles corresponding to gene lengths. Maximum relative expression: the maximum fraction of total MHC-I expression (FPKM) attributable to a sequence across all RNA...
  2. Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
    • Julie A. Karl,
    • Trent M. Prall,
    • Hailey E. Bussan,
    • Joshua M. Varghese,
    • Aparna Pal,
    • Roger W. Wiseman,
    • and David H. O'Connor
    Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
    ...et al. 2006). Extensive sequencing of MHC-I transcript and genomic DNA PCR amplicons suggests that this expansion of MHC-B genes is common in both rhesus and cynomolgus macaques (Otting et al. 2005; Doxiadis et al. 2013; Wiseman et al. 2013; Karl et al. 2017; Shortreed et al. 2020). These MHC...
  3. Research: Targeted and complete genomic sequencing of the major histocompatibility complex in haplotypic form of individual heterozygous samples
    • Taishan Hu,
    • Timothy L. Mosbruger,
    • Nikolaos G. Tairis,
    • Amalia Dinou,
    • Pushkala Jayaraman,
    • Mahdi Sarmady,
    • Kingham Brewster,
    • Yang Li,
    • Tristan J. Hayeck,
    • Jamie L. Duke,
    • and Dimitri S. Monos
    Genome Res. October 2024 34: 1500-1513; Published in Advance September 26, 2024, doi:10.1101/gr.278588.123
    ...Fi assemblies to compare with our work. Forty-five out of 70 haplotypes were complete across the MHC, the remaining 25 had one or more breaks in the MHC. The most common breaks in the 1KGP samples were across the HLA-DR region (14/70) and the RCCX region (10/70). There were seven breaks outside of the two...
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  4. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...to address tagged sequences of the medically relevant and complete autosomal genes. The 389 gene panel was extensively compared to whole- sequencing using 11 control samples. While the technical performance of the panel using PacBio yielded good results, the authors noted that 75% of the genes lacked Clin...
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  5. Method: Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing
    • Charles Cole,
    • Ashley Byrne,
    • Matthew Adams,
    • Roger Volden,
    • and Christopher Vollmers
    Genome Res. April 2020 30: 589-601; Published in Advance April 20, 2020, doi:10.1101/gr.257188.119
    ...determine the sequence and identity of alleles of HLA genes. HLA genes encode for the major histocompatibility complex (MHC) group of immune receptors which are instrumental in the presentation of antigens on the cell surface (Shiina et al. 2009). Determining the identities of HLA alleles that are present...
  6. Method: Full-resolution HLA and KIR gene annotations for human genome assemblies
    • Ying Zhou,
    • Li Song,
    • and Heng Li
    Genome Res. November 2024 34: 1931-1941; Published in Advance June 5, 2024, doi:10.1101/gr.278985.124
    ...on a permutation test (Methods). This observation is probably caused by balancing selection that tends to maintain the high diversity in MHC.HLA gene deletionsDeletion of HLA-Y (Y-del) is the most common gene deletion among HLA genes (71.3% in HPRC and 87.3% in CPC). It is rarely studied in large cohorts because...
  7. Method: A complete pedigree-based graph workflow for rare candidate variant analysis
    • Charles Markello,
    • Charles Huang,
    • Alex Rodriguez,
    • Andrew Carroll,
    • Pi-Chuan Chang,
    • Jordan Eizenga,
    • Thomas Markello,
    • David Haussler,
    • and Benedict Paten
    Genome Res. May 2022 32: 893-903; Published in Advance April 28, 2022, doi:10.1101/gr.276387.121
    ...are then called using DeepTrio (Fig. 1B; The 1000 Genomes Project Consortium 2015; Sirén et al. 2021). Next, variants in 1000 Genomes Project haplotypes that appear missing in the DeepTrio-called variants are imputed. The purpose of this is to fill in common variants that were possibly missed by the variant...
  8. Method: Efficient and accurate KIR and HLA genotyping with massively parallel sequencing data
    • Li Song,
    • Gali Bai,
    • X. Shirley Liu,
    • Bo Li,
    • and Heng Li
    Genome Res. May 11, 2023 gr.277585.122; Published in Advance May 11, 2023, doi:10.1101/gr.277585.122
    ...may open the opportunity for HLA and KIR genotyping across various sequencing applications. Introduction Polymorphisms in immune receptor genes diversify the immune response, which strengthens the resilience of a population to diseases. In particular, major histocompatibility complex (MHC) encoded...
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  9. Research: Alu insertion variants alter gene transcript levels
    • Lindsay M. Payer,
    • Jared P. Steranka,
    • Maria S. Kryatova,
    • Giacomo Grillo,
    • Mathieu Lupien,
    • Pedro P. Rocha,
    • and Kathleen H. Burns
    Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
    ...occur in the 114 bp common to the two sequences (see the previous section for putative TFBS in this region).View larger version: In this window In a new window Figure 5. Mechanisms for how Alu insertion polymorphisms associated with breast cancer affect gene expression levels. For each of four loci (A...
  10. Resource: Assembly and analysis of 100 full MHC haplotypes from the Danish population
    • Jacob M. Jensen,
    • Palle Villesen,
    • Rune M. Friborg,
    • The Danish Pan-Genome Consortium,
    • Thomas Mailund,
    • Søren Besenbacher,
    • and Mikkel H. Schierup
    Genome Res. September 2017 27: 1597-1607; Published in Advance August 3, 2017, doi:10.1101/gr.218891.116
    ...that alignment to the reference haplotype (pgf) near the C4A and C4B genes (Chr 6: 31982024–32002681, Chr 6: 32014762–32035418, blue gene markers in Fig. 2), known to harbor common structural variation and to be associated with several diseases, is poor for most haplotypes including the alternative reference...
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